{"code":"SASDCH7","status":"Published","type_of_curve":"Single concentration","angular_unit":"1/A","project":{"title":"Production, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis.","publication":{"title":"Production, biophysical characterization and initial crystallization studies of the N- and C-terminal domains of DsbD, an essential enzyme in Neisseria meningitidis.","author_list":"Smith RP, Whitten AE, Paxman JJ, Kahler CM, Scanlon MJ, Heras B","journal":"Acta Crystallogr F Struct Biol Commun","doi":"10.1107/S2053230X17017800","pmid":"29372905","published_date":"2018 Jan 1"},"status":"released","submitted_date":"2017-09-13","released_date":"2018-01-03"},"pddf_data":"https://www.sasbdb.org/media/p_of_R_files/SASDCH7.out","intensities_data":"https://www.sasbdb.org/media/intensities_files/SASDCH7.dat","intensities_log_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCH7_dat_img.png","intensities_kratky_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCH7_kratky_img.png","pddf_plot":"https://www.sasbdb.org/media/p_of_R_files/pofr_images/SASDCH7_pofr_img.png","intensities_guinier_plot":"https://www.sasbdb.org/media/intensities_files/scattering_plots/SASDCH7_guinier_img.png","sascif_data":"https://www.sasbdb.org/media/sascif/sascif_files/SASDCH7.sascif","experiment":{"instrument":{"detector":{"type":"Dectris","name":"Pilatus 1M","resolution":172.0},"name":"Australian  Synchrotron","city":"Melbourne","country":"Australia","beamline_name":"SAXS/WAXS","beam_geometry":"Point","type_of_source":"X-ray synchrotron","point_source":true,"line_collimation":null,"sample_path_length":null,"line_collimation_slitlength":null,"line_collimation_integrationwidth":null,"xray_energy":null,"beam_profile_ah":null,"beam_profile_al":null},"sample":{"molecule":[{"long_name":"N-terminus of disulfide interchange protein DsbD","short_name":"n-DsbD","sequence":"SNANDLLPPEKAFVPELAVADDGVNVRFRIADGYYMYQAKIVGKTDPADLLGQPSFSKGEEKEDEFFGRQTVYHHEAQVAFPYAKAVGEPYKLVLTYQGCAEVGVCYPPVDTEFDISGNGTYHPQT","organism":"Neisseria meningitidis","uniprot_code":"Q9JTL9","uniprot_range_first":23,"uniprot_range_last":146,"oligomerization":"monomer","molecular_type":"protein","uniprot_sequence":"MKKLICLFAVFLMLCGRAFALDANDLLPPEKAFVPELAVADDGVNVRFRIADGYYMYQAK\nIVGKTDPADLLGQPSFSKGEEKEDEFFGRQTVYHHEAQVAFPYAKAVGEPYKLVLTYQGC\nAEAGVCYPPVDTEFDISGNGTYHPQTDEPASAKDRFLQPSSQNGSGALPPPKGDEGGDSR\nFKLSWDTLNANLLAFFLAGLGLSFTACMYPLLPIVSSIVVGDKKAGKARAFVLSVVYVQG\nLSLTYTLVGIVAGLTGALLTVWLQQAWVVLAASALMVVLALSMFGLFNIQLPNAVQSYFQ\nNQSSRLSGGKIVSVFIMGILSALIVGPCVAPPLAFALGYIGQTGDAVLGGLALYTLALGT\nGVPLIAIGTFGGHILPRAGDWMNAVKYAFGFILLAVAVYLATPHLPYYLVVALYTLLMLV\nPACMLLVNGRRQKRRPKAVAFALGGILLIGGAWFGWQGANGKTTALHHFLTLNPPAEAGK\nSSEHGKMFADTAALKAAMDTALKEHPDKPVVLDFYADWCISCKEMAAYTLNQPEVHQAVD\nMERFFQIDVTANTPEHQALLKEYGLFGPPGVFVVRSDGSRSEPLLGFVKADKFIEWYEQN\nR","mw":13.911,"total_mw":13.911,"number_molecules":1,"complex_state":false,"deuteration":null,"molecule_source":"biological","molecule_description":null}],"buffer":{"name":"25mM HEPES 150mM NaCl","concentration_unit":null,"comment":null,"additive":null,"concentration":null,"pka":null,"ph":6.7,"deuteration":null},"purity_method":null,"name":"N-terminal domain of DsbD from N. meningitidis","ext_coefficient":null,"contrast":null,"specific_vol":null,"dry_vol":null,"absorbption":null,"deuteration":null,"mixture":null},"contributor":[{"affiliation":[{"short_name":"ANSTO","address":"Kirrawee DC, NSW 2232, Australia","full_name":"Australian Nuclear Science and Technology Organisation","webpage":""}],"contributor_name":"Andrew","contributor_surname":"Whitten","orcid":null}],"concentration_method":null,"concentration_unit":null,"date":"2013-05-04","storage_temperature":4.0,"cell_temperature":12.0,"exposure_time":2.0,"number_of_frames":30,"wavelength":0.1127,"sample_detector_distance":1.48,"concentration_min":0.4,"concentration_max":5.9,"sample_volume":null,"flow_rate":null,"s_min":0.136,"s_max":3.99,"total_exposure_time":null,"seccolumn":null},"fits":[{"models":[{"model_plot":"https://www.sasbdb.org/media/pdb_file/images/SASDCH7_fit1_model1_img.png","software":"DAMMIN","pdb_link":[],"model_title":null,"type_of_model":"dummy","software_version":"5.3","model_data":"https://www.sasbdb.org/media/pdb_file/SASDCH7_fit1_model1.pdb","model_mw":12.131,"bead_radius":1.5,"log":"https://www.sasbdb.org/media/log_files/damsel_ZE5wX89.log","symmetry":"","comment":"","user":111}],"fit_unit":"1/A","fit_plot":"https://www.sasbdb.org/media/fitting_files/scattering_plots/SASDCH7_fit1_fit_img.png","software":"DAMMIN","chi_square_value":1.899,"p_value":0.0,"fit_residual_plot":"SASDCH7_fit1_fitresiduals_img.png","fit_data":"https://www.sasbdb.org/media/fitting_files/SASDCH7_fit1.fir","fit_log":"https://www.sasbdb.org/media/fitting_files/log_files/run3.log","software_version":"5.3","description":null}],"estimated_volume_method":null,"pddf_software":"ATSAS GNOM","pddf_software_version":"4.6","i0_calibration_standard":null,"description":null,"experiment_description":"X-ray synchrotron radiation scattering data from solutions of the n-terminal domain of DsbD from Neisseria meningitidis in 25 mM HEPES 150mM NaCl pH 6.7 were collected on the SAXS/WAXS beam line of the Australian Synchrotron (Melbourne, Australia) using a 2D Photon counting Pilatus 1M-W pixel detector (I(s) vs s, where s = 4π sin θ/λ and 2θ is the scattering angle; λ=0.1127 nm). Thirty successive 2 second frames were collected across solute concentrations of 0.4-5.9 mg/ml. The SAXS data displayed this entry was derived from a 0.74 mg/ml sample as it was deemed to be the highest concentration at which the effects of concentration were negligible. The Rg for n-NmDsbD showed mild concentration dependence above a concentration of 1.0 mg/mL, dropping from ~17.5 Å at 0.4 mg/mL to ~16 Å at 5.9 mg/mL. The data were normalized to the intensity of the transmitted beam and radially averaged and the scattering of the solvent-blank was subtracted. The models and corresponding fits include those derived from dummy-atom modelling using DAMMIN.","tags":[],"intensity_unit":"1/cm","experimental_mw":13.2,"experimental_mw_error":null,"guinier_i0_mw":13.2,"guinier_i0_mw_error":1.0,"porod_mw":14.2,"porod_mw_error":null,"pddf_i0":0.007688,"pddf_i0_error":1.2e-05,"guinier_i0":0.00776,"guinier_i0_error":3e-05,"pddf_rg":1.73,"pddf_rg_error":0.1,"guinier_rg":1.76,"guinier_rg_error":0.02,"pddf_dmax":5.7,"pddf_dmax_error":0.3,"porod_volume":17.3,"porod_volume_error":null,"estimated_volume":null,"estimated_volume_error":null,"guinier_point_first":3,"guinier_point_last":37,"pddf_point_first":null,"pddf_point_last":null,"i0_calibration_standard_data":null,"intensities_log_log_plot":"SASDCH7_datloglog_img.png","symmetry":null,"last_modified":"2019-12-06T13:07:15.624532+01:00","bragg_peak":[]}